Hands-on Exercise 10

Published

October 14, 2024

Modified

October 15, 2024

1.0 Overview

1.1 Objectives

1.2 The Data

Two data sets will be used in this model building exercise, they are:

  • URA Master Plan subzone boundary in shapefile format (i.e. MP14_SUBZONE_WEB_PL)

  • condo_resale_2015 in csv format (i.e. condo_resale_2015.csv)

1.3 Getting Started

Before we get started, it is important for us to install the necessary R packages into R and launch these R packages into R environment.

The R packages needed for this exercise are as follows:

  • R package for building OLS and performing diagnostics tests

  • R package for calibrating geographical weighted family of models

  • R package for multivariate data visualisation and analysis

  • Spatial data handling

    • sf
  • Attribute data handling

    • tidyverse, especially readr, ggplot2 and dplyr
  • Choropleth mapping

    • tmap
pacman::p_load(olsrr, corrplot, ggpubr, sf, spdep, GWmodel, tmap, tidyverse, gtsummary)

2.0 Geospatial Data Wrangling

2.1 Importing Geospatial Data

The code chunk below is used to import MP_SUBZONE_WEB_PL shapefile by using st_read() of sf packages.

mpsz = st_read(dsn = "data/geospatial", layer = "MP14_SUBZONE_WEB_PL")
Reading layer `MP14_SUBZONE_WEB_PL' from data source 
  `/Users/jezelei/jezeleii/IS415-GA/Hands-On_Exercise/Hands-on_Ex10/data/geospatial' 
  using driver `ESRI Shapefile'
Simple feature collection with 323 features and 15 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 2667.538 ymin: 15748.72 xmax: 56396.44 ymax: 50256.33
Projected CRS: SVY21

2.2 Updating CRS Information

The code chunk below updates the newly imported mpsz with the correct ESPG code (i.e. 3414)

mpsz_svy21 <- st_transform(mpsz, 3414)

After transforming the projection metadata, you can varify the projection of the newly transformed mpsz_svy21 by using st_crs() of sf package.

The code chunk below will be used to varify the newly transformed mpsz_svy21.

st_crs(mpsz_svy21)
Coordinate Reference System:
  User input: EPSG:3414 
  wkt:
PROJCRS["SVY21 / Singapore TM",
    BASEGEOGCRS["SVY21",
        DATUM["SVY21",
            ELLIPSOID["WGS 84",6378137,298.257223563,
                LENGTHUNIT["metre",1]]],
        PRIMEM["Greenwich",0,
            ANGLEUNIT["degree",0.0174532925199433]],
        ID["EPSG",4757]],
    CONVERSION["Singapore Transverse Mercator",
        METHOD["Transverse Mercator",
            ID["EPSG",9807]],
        PARAMETER["Latitude of natural origin",1.36666666666667,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8801]],
        PARAMETER["Longitude of natural origin",103.833333333333,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8802]],
        PARAMETER["Scale factor at natural origin",1,
            SCALEUNIT["unity",1],
            ID["EPSG",8805]],
        PARAMETER["False easting",28001.642,
            LENGTHUNIT["metre",1],
            ID["EPSG",8806]],
        PARAMETER["False northing",38744.572,
            LENGTHUNIT["metre",1],
            ID["EPSG",8807]]],
    CS[Cartesian,2],
        AXIS["northing (N)",north,
            ORDER[1],
            LENGTHUNIT["metre",1]],
        AXIS["easting (E)",east,
            ORDER[2],
            LENGTHUNIT["metre",1]],
    USAGE[
        SCOPE["Cadastre, engineering survey, topographic mapping."],
        AREA["Singapore - onshore and offshore."],
        BBOX[1.13,103.59,1.47,104.07]],
    ID["EPSG",3414]]

We reveal the extent of mpsz_svy21 by using st_bbox() of the sf package.

st_bbox(mpsz_svy21)
     xmin      ymin      xmax      ymax 
 2667.538 15748.721 56396.440 50256.334 

3.0 Aspatial Data Wrangling

3.1 Importing the aspatial data

The condo_resale_2015 is in csv file format. The codes chunk below uses read_csv() function of readr package to import condo_resale_2015 into R as a tibble data frame called condo_resale.

condo_resale = read_csv("data/aspatial/Condo_resale_2015.csv")
Rows: 1436 Columns: 23
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
dbl (23): LATITUDE, LONGITUDE, POSTCODE, SELLING_PRICE, AREA_SQM, AGE, PROX_...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

After importing the data file into R, it is important for us to examine if the data file has been imported correctly.

The codes chunks below uses glimpse() to display the data structure of will do the job.

glimpse(condo_resale)
Rows: 1,436
Columns: 23
$ LATITUDE             <dbl> 1.287145, 1.328698, 1.313727, 1.308563, 1.321437,…
$ LONGITUDE            <dbl> 103.7802, 103.8123, 103.7971, 103.8247, 103.9505,…
$ POSTCODE             <dbl> 118635, 288420, 267833, 258380, 467169, 466472, 3…
$ SELLING_PRICE        <dbl> 3000000, 3880000, 3325000, 4250000, 1400000, 1320…
$ AREA_SQM             <dbl> 309, 290, 248, 127, 145, 139, 218, 141, 165, 168,…
$ AGE                  <dbl> 30, 32, 33, 7, 28, 22, 24, 24, 27, 31, 17, 22, 6,…
$ PROX_CBD             <dbl> 7.941259, 6.609797, 6.898000, 4.038861, 11.783402…
$ PROX_CHILDCARE       <dbl> 0.16597932, 0.28027246, 0.42922669, 0.39473543, 0…
$ PROX_ELDERLYCARE     <dbl> 2.5198118, 1.9333338, 0.5021395, 1.9910316, 1.121…
$ PROX_URA_GROWTH_AREA <dbl> 6.618741, 7.505109, 6.463887, 4.906512, 6.410632,…
$ PROX_HAWKER_MARKET   <dbl> 1.76542207, 0.54507614, 0.37789301, 1.68259969, 0…
$ PROX_KINDERGARTEN    <dbl> 0.05835552, 0.61592412, 0.14120309, 0.38200076, 0…
$ PROX_MRT             <dbl> 0.5607188, 0.6584461, 0.3053433, 0.6910183, 0.528…
$ PROX_PARK            <dbl> 1.1710446, 0.1992269, 0.2779886, 0.9832843, 0.116…
$ PROX_PRIMARY_SCH     <dbl> 1.6340256, 0.9747834, 1.4715016, 1.4546324, 0.709…
$ PROX_TOP_PRIMARY_SCH <dbl> 3.3273195, 0.9747834, 1.4715016, 2.3006394, 0.709…
$ PROX_SHOPPING_MALL   <dbl> 2.2102717, 2.9374279, 1.2256850, 0.3525671, 1.307…
$ PROX_SUPERMARKET     <dbl> 0.9103958, 0.5900617, 0.4135583, 0.4162219, 0.581…
$ PROX_BUS_STOP        <dbl> 0.10336166, 0.28673408, 0.28504777, 0.29872340, 0…
$ NO_Of_UNITS          <dbl> 18, 20, 27, 30, 30, 31, 32, 32, 32, 32, 34, 34, 3…
$ FAMILY_FRIENDLY      <dbl> 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0…
$ FREEHOLD             <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1…
$ LEASEHOLD_99YR       <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
summary(condo_resale)
    LATITUDE       LONGITUDE        POSTCODE      SELLING_PRICE     
 Min.   :1.240   Min.   :103.7   Min.   : 18965   Min.   :  540000  
 1st Qu.:1.309   1st Qu.:103.8   1st Qu.:259849   1st Qu.: 1100000  
 Median :1.328   Median :103.8   Median :469298   Median : 1383222  
 Mean   :1.334   Mean   :103.8   Mean   :440439   Mean   : 1751211  
 3rd Qu.:1.357   3rd Qu.:103.9   3rd Qu.:589486   3rd Qu.: 1950000  
 Max.   :1.454   Max.   :104.0   Max.   :828833   Max.   :18000000  
    AREA_SQM          AGE           PROX_CBD       PROX_CHILDCARE    
 Min.   : 34.0   Min.   : 0.00   Min.   : 0.3869   Min.   :0.004927  
 1st Qu.:103.0   1st Qu.: 5.00   1st Qu.: 5.5574   1st Qu.:0.174481  
 Median :121.0   Median :11.00   Median : 9.3567   Median :0.258135  
 Mean   :136.5   Mean   :12.14   Mean   : 9.3254   Mean   :0.326313  
 3rd Qu.:156.0   3rd Qu.:18.00   3rd Qu.:12.6661   3rd Qu.:0.368293  
 Max.   :619.0   Max.   :37.00   Max.   :19.1804   Max.   :3.465726  
 PROX_ELDERLYCARE  PROX_URA_GROWTH_AREA PROX_HAWKER_MARKET PROX_KINDERGARTEN 
 Min.   :0.05451   Min.   :0.2145       Min.   :0.05182    Min.   :0.004927  
 1st Qu.:0.61254   1st Qu.:3.1643       1st Qu.:0.55245    1st Qu.:0.276345  
 Median :0.94179   Median :4.6186       Median :0.90842    Median :0.413385  
 Mean   :1.05351   Mean   :4.5981       Mean   :1.27987    Mean   :0.458903  
 3rd Qu.:1.35122   3rd Qu.:5.7550       3rd Qu.:1.68578    3rd Qu.:0.578474  
 Max.   :3.94916   Max.   :9.1554       Max.   :5.37435    Max.   :2.229045  
    PROX_MRT         PROX_PARK       PROX_PRIMARY_SCH  PROX_TOP_PRIMARY_SCH
 Min.   :0.05278   Min.   :0.02906   Min.   :0.07711   Min.   :0.07711     
 1st Qu.:0.34646   1st Qu.:0.26211   1st Qu.:0.44024   1st Qu.:1.34451     
 Median :0.57430   Median :0.39926   Median :0.63505   Median :1.88213     
 Mean   :0.67316   Mean   :0.49802   Mean   :0.75471   Mean   :2.27347     
 3rd Qu.:0.84844   3rd Qu.:0.65592   3rd Qu.:0.95104   3rd Qu.:2.90954     
 Max.   :3.48037   Max.   :2.16105   Max.   :3.92899   Max.   :6.74819     
 PROX_SHOPPING_MALL PROX_SUPERMARKET PROX_BUS_STOP       NO_Of_UNITS    
 Min.   :0.0000     Min.   :0.0000   Min.   :0.001595   Min.   :  18.0  
 1st Qu.:0.5258     1st Qu.:0.3695   1st Qu.:0.098356   1st Qu.: 188.8  
 Median :0.9357     Median :0.5687   Median :0.151710   Median : 360.0  
 Mean   :1.0455     Mean   :0.6141   Mean   :0.193974   Mean   : 409.2  
 3rd Qu.:1.3994     3rd Qu.:0.7862   3rd Qu.:0.220466   3rd Qu.: 590.0  
 Max.   :3.4774     Max.   :2.2441   Max.   :2.476639   Max.   :1703.0  
 FAMILY_FRIENDLY     FREEHOLD      LEASEHOLD_99YR  
 Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
 1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.0000  
 Median :0.0000   Median :0.0000   Median :0.0000  
 Mean   :0.4868   Mean   :0.4227   Mean   :0.4882  
 3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:1.0000  
 Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
head(condo_resale$LONGITUDE)
[1] 103.7802 103.8123 103.7971 103.8247 103.9505 103.9386
head(condo_resale$LATITUDE)
[1] 1.287145 1.328698 1.313727 1.308563 1.321437 1.314198

3.2 Converting aspatial data frame into an sf object

The code chunk below converts condo_resale data frame into a simple feature data frame by using st_as_sf() of sf packages.

condo_resale.sf <- st_as_sf(condo_resale, 
                            coords = c("LONGITUDE", "LATITUDE"),
                            crs=4326) %>%
  st_transform(crs=3414)

st_crs(condo_resale.sf)
Coordinate Reference System:
  User input: EPSG:3414 
  wkt:
PROJCRS["SVY21 / Singapore TM",
    BASEGEOGCRS["SVY21",
        DATUM["SVY21",
            ELLIPSOID["WGS 84",6378137,298.257223563,
                LENGTHUNIT["metre",1]]],
        PRIMEM["Greenwich",0,
            ANGLEUNIT["degree",0.0174532925199433]],
        ID["EPSG",4757]],
    CONVERSION["Singapore Transverse Mercator",
        METHOD["Transverse Mercator",
            ID["EPSG",9807]],
        PARAMETER["Latitude of natural origin",1.36666666666667,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8801]],
        PARAMETER["Longitude of natural origin",103.833333333333,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8802]],
        PARAMETER["Scale factor at natural origin",1,
            SCALEUNIT["unity",1],
            ID["EPSG",8805]],
        PARAMETER["False easting",28001.642,
            LENGTHUNIT["metre",1],
            ID["EPSG",8806]],
        PARAMETER["False northing",38744.572,
            LENGTHUNIT["metre",1],
            ID["EPSG",8807]]],
    CS[Cartesian,2],
        AXIS["northing (N)",north,
            ORDER[1],
            LENGTHUNIT["metre",1]],
        AXIS["easting (E)",east,
            ORDER[2],
            LENGTHUNIT["metre",1]],
    USAGE[
        SCOPE["Cadastre, engineering survey, topographic mapping."],
        AREA["Singapore - onshore and offshore."],
        BBOX[1.13,103.59,1.47,104.07]],
    ID["EPSG",3414]]

Notice that st_transform() of sf package is used to convert the coordinates from wgs84 (i.e. crs:4326) to svy21 (i.e. crs=3414).

Next, head() is used to list the content of condo_resale.sf object.

head(condo_resale.sf)
Simple feature collection with 6 features and 21 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: 22085.12 ymin: 29951.54 xmax: 41042.56 ymax: 34546.2
Projected CRS: SVY21 / Singapore TM
# A tibble: 6 × 22
  POSTCODE SELLING_PRICE AREA_SQM   AGE PROX_CBD PROX_CHILDCARE PROX_ELDERLYCARE
     <dbl>         <dbl>    <dbl> <dbl>    <dbl>          <dbl>            <dbl>
1   118635       3000000      309    30     7.94          0.166            2.52 
2   288420       3880000      290    32     6.61          0.280            1.93 
3   267833       3325000      248    33     6.90          0.429            0.502
4   258380       4250000      127     7     4.04          0.395            1.99 
5   467169       1400000      145    28    11.8           0.119            1.12 
6   466472       1320000      139    22    10.3           0.125            0.789
# ℹ 15 more variables: PROX_URA_GROWTH_AREA <dbl>, PROX_HAWKER_MARKET <dbl>,
#   PROX_KINDERGARTEN <dbl>, PROX_MRT <dbl>, PROX_PARK <dbl>,
#   PROX_PRIMARY_SCH <dbl>, PROX_TOP_PRIMARY_SCH <dbl>,
#   PROX_SHOPPING_MALL <dbl>, PROX_SUPERMARKET <dbl>, PROX_BUS_STOP <dbl>,
#   NO_Of_UNITS <dbl>, FAMILY_FRIENDLY <dbl>, FREEHOLD <dbl>,
#   LEASEHOLD_99YR <dbl>, geometry <POINT [m]>

4.0 Exploratory Data Analysis

4.1 EDA using statistical graphs

We can plot the distribution of SELLING_PRICE by using appropriate Exploratory Data Analysis (EDA) as shown in the code chunk below.

ggplot(data=condo_resale.sf, aes(x=`SELLING_PRICE`)) + 
  geom_histogram(bins=20, color="black", fill="light blue")

The figure above reveals a right skewed distribution. This means that more condominium units were transacted at relative lower prices.

Statistically, the skewed dsitribution can be normalised by using log transformation. The code chunk below is used to derive a new variable called LOG_SELLING_PRICE by using a log transformation on the variable SELLING_PRICE. It is performed using mutate() of dplyr package.

condo_resale.sf <- condo_resale.sf %>% 
  mutate(`LOG_SELLING_PRICE` = log(SELLING_PRICE))

We can plot LOG_SELLING_PRICE using the code chunk below:

ggplot(data=condo_resale.sf, aes(x=`LOG_SELLING_PRICE`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

The distribution is relatively less skewed after transformation

4.2 Multiple Histogram Plots distribution of variables

The code chunk below is used to create 12 histograms. Then, ggarrange() is used to organised these histogram into a 3 columns by 4 rows small multiple plot.

AREA_SQM <- ggplot(data=condo_resale.sf, aes(x= `AREA_SQM`)) + 
  geom_histogram(bins=20, color="black", fill="light blue")

AGE <- ggplot(data=condo_resale.sf, aes(x= `AGE`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_CBD <- ggplot(data=condo_resale.sf, aes(x= `PROX_CBD`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_CHILDCARE <- ggplot(data=condo_resale.sf, aes(x= `PROX_CHILDCARE`)) + 
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_ELDERLYCARE <- ggplot(data=condo_resale.sf, aes(x= `PROX_ELDERLYCARE`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_URA_GROWTH_AREA <- ggplot(data=condo_resale.sf, 
                               aes(x= `PROX_URA_GROWTH_AREA`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_HAWKER_MARKET <- ggplot(data=condo_resale.sf, aes(x= `PROX_HAWKER_MARKET`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_KINDERGARTEN <- ggplot(data=condo_resale.sf, aes(x= `PROX_KINDERGARTEN`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_MRT <- ggplot(data=condo_resale.sf, aes(x= `PROX_MRT`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_PARK <- ggplot(data=condo_resale.sf, aes(x= `PROX_PARK`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_PRIMARY_SCH <- ggplot(data=condo_resale.sf, aes(x= `PROX_PRIMARY_SCH`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

PROX_TOP_PRIMARY_SCH <- ggplot(data=condo_resale.sf, 
                               aes(x= `PROX_TOP_PRIMARY_SCH`)) +
  geom_histogram(bins=20, color="black", fill="light blue")

ggarrange(AREA_SQM, AGE, PROX_CBD, PROX_CHILDCARE, PROX_ELDERLYCARE, 
          PROX_URA_GROWTH_AREA, PROX_HAWKER_MARKET, PROX_KINDERGARTEN, PROX_MRT,
          PROX_PARK, PROX_PRIMARY_SCH, PROX_TOP_PRIMARY_SCH,  
          ncol = 3, nrow = 4)

4.3 Drawing Statistical Point Map

Lastly, we want to reveal the geospatial distribution condominium resale prices in Singapore. The map will be prepared by using tmap package.

First, we will turn on the interactive mode of tmap by using the code chunk below.

tmap_mode("view")
tmap mode set to interactive viewing

Next, the code chunks below is used to create an interactive point symbol map.

tm_shape(mpsz_svy21) + 
  tm_polygons() + 
  tm_shape(condo_resale.sf) + 
  tm_dots(col="SELLING_PRICE", 
          alpha = 0.6, 
          style="quantile") + 
  tm_view(set.zoom.limits = c(11,14)) + 
  tmap_options(check.and.fix=TRUE) 
Warning: The shape mpsz_svy21 is invalid (after reprojection). See
sf::st_is_valid

Notice that tm_dots() is used instead of tm_bubbles().

set.zoom.limits argument of tm_view() sets the minimum and maximum zoom level to 11 and 14 respectively.

tm_shape(mpsz_svy21) + 
  tm_polygons() + 
  tm_shape(condo_resale.sf) + 
  tm_bubbles(col="SELLING_PRICE", 
          alpha = 0.6, 
          style="quantile") + 
  tm_view(set.zoom.limits = c(11,14)) + 
  tmap_options(check.and.fix=TRUE) 
Warning: The shape mpsz_svy21 is invalid (after reprojection). See
sf::st_is_valid

Before moving on to the next section, the code below will be used to turn R display into plot mode.

tmap_mode("plot")
tmap mode set to plotting

5.0 Hedonic Pricing Modelling in R

5.1 Simple Linear Regression Method

First, we will build a simple linear regression model by using SELLING_PRICE as the dependent variable and AREA_SQM as the independent variable.

condo.slr <- lm(formula=SELLING_PRICE ~ AREA_SQM, data = condo_resale.sf)

lm() returns an object of class “lm” or for multiple responses of class c(“mlm”, “lm”).

The functions summary() and anova() can be used to obtain and print a summary and analysis of variance table of the results. The generic accessor functions coefficients, effects, fitted.values and residuals extract various useful features of the value returned by lm.

summary(condo.slr)

Call:
lm(formula = SELLING_PRICE ~ AREA_SQM, data = condo_resale.sf)

Residuals:
     Min       1Q   Median       3Q      Max 
-3695815  -391764   -87517   258900 13503875 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) -258121.1    63517.2  -4.064 5.09e-05 ***
AREA_SQM      14719.0      428.1  34.381  < 2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 942700 on 1434 degrees of freedom
Multiple R-squared:  0.4518,    Adjusted R-squared:  0.4515 
F-statistic:  1182 on 1 and 1434 DF,  p-value: < 2.2e-16

The output report reveals that the SELLING_PRICE can be explained by using the formula:

      *y = -258121.1 + 14719x1*

The R-squared of 0.4518 reveals that the simple regression model built is able to explain about 45% of the resale prices.

Since p-value is much smaller than 0.0001, we will reject the null hypothesis that mean is a good estimator of SELLING_PRICE. This will allow us to infer that simple linear regression model above is a good estimator of SELLING_PRICE.

The Coefficients: section of the report reveals that the p-values of both the estimates of the Intercept and ARA_SQM are smaller than 0.001. In view of this, the null hypothesis of the B0 and B1 are equal to 0 will be rejected. As a results, we will be able to infer that the B0 and B1 are good parameter estimates.

To visualise the best fit curve on a scatterplot, we can incorporate lm() as a method function in ggplot’s geometry as shown in the code chunk below.

ggplot(data = condo_resale.sf, 
       aes(x=`AREA_SQM`, y=`SELLING_PRICE`)) + 
  geom_point() +
  geom_smooth(method=lm)
`geom_smooth()` using formula = 'y ~ x'


Figure above reveals that there are a few statistical outliers with relatively high selling prices.

5.2 Multiple Linear Regression Method

5.2.1 Visualising the relationships of the independent variables

Before building a multiple regression model, it is important to ensure that the indepdent variables used are not highly correlated to each other. If these highly correlated independent variables are used in building a regression model by mistake, the quality of the model will be compromised. This phenomenon is known as multicollinearity in statistics.

Correlation matrix is commonly used to visualise the relationships between the independent variables. Beside the pairs() of R, there are many packages support the display of a correlation matrix. In this section, the corrplot package will be used.

The code chunk below is used to plot a scatterplot matrix of the relationship between the independent variables in condo_resale data.frame.

corrplot(cor(condo_resale[, 1:23]), diag=FALSE,order="AOE",
         tl.pos="td", tl.cex=0.5, method="number", type="upper")

Matrix reorder is very important for mining the hiden structure and patter in the matrix. There are four methods in corrplot (parameter order), named “AOE”, “FPC”, “hclust”, “alphabet”. In the code chunk above, AOE order is used. It orders the variables by using the angular order of the eigenvectors method suggested by Michael Friendly.

From the scatterplot matrix, it is clear that Freehold is highly correlated to LEASE_99YEAR. In view of this, it is wiser to only include either one of them in the subsequent model building. As a result, LEASE_99YEAR is excluded in the subsequent model building.

5.3 Building a hedonic pricing model using multiple linear regression method

The code chunk below using lm() to calibrate the multiple linear regression model.

condo.mlr <- lm(formula = SELLING_PRICE ~ AREA_SQM + AGE    + 
                  PROX_CBD + PROX_CHILDCARE + PROX_ELDERLYCARE +
                  PROX_URA_GROWTH_AREA + PROX_HAWKER_MARKET + PROX_KINDERGARTEN + 
                  PROX_MRT  + PROX_PARK + PROX_PRIMARY_SCH + 
                  PROX_TOP_PRIMARY_SCH + PROX_SHOPPING_MALL + PROX_SUPERMARKET + 
                  PROX_BUS_STOP + NO_Of_UNITS + FAMILY_FRIENDLY + FREEHOLD, 
                data=condo_resale.sf)
summary(condo.mlr)

Call:
lm(formula = SELLING_PRICE ~ AREA_SQM + AGE + PROX_CBD + PROX_CHILDCARE + 
    PROX_ELDERLYCARE + PROX_URA_GROWTH_AREA + PROX_HAWKER_MARKET + 
    PROX_KINDERGARTEN + PROX_MRT + PROX_PARK + PROX_PRIMARY_SCH + 
    PROX_TOP_PRIMARY_SCH + PROX_SHOPPING_MALL + PROX_SUPERMARKET + 
    PROX_BUS_STOP + NO_Of_UNITS + FAMILY_FRIENDLY + FREEHOLD, 
    data = condo_resale.sf)

Residuals:
     Min       1Q   Median       3Q      Max 
-3475964  -293923   -23069   241043 12260381 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)    
(Intercept)           481728.40  121441.01   3.967 7.65e-05 ***
AREA_SQM               12708.32     369.59  34.385  < 2e-16 ***
AGE                   -24440.82    2763.16  -8.845  < 2e-16 ***
PROX_CBD              -78669.78    6768.97 -11.622  < 2e-16 ***
PROX_CHILDCARE       -351617.91  109467.25  -3.212  0.00135 ** 
PROX_ELDERLYCARE      171029.42   42110.51   4.061 5.14e-05 ***
PROX_URA_GROWTH_AREA   38474.53   12523.57   3.072  0.00217 ** 
PROX_HAWKER_MARKET     23746.10   29299.76   0.810  0.41782    
PROX_KINDERGARTEN     147468.99   82668.87   1.784  0.07466 .  
PROX_MRT             -314599.68   57947.44  -5.429 6.66e-08 ***
PROX_PARK             563280.50   66551.68   8.464  < 2e-16 ***
PROX_PRIMARY_SCH      180186.08   65237.95   2.762  0.00582 ** 
PROX_TOP_PRIMARY_SCH    2280.04   20410.43   0.112  0.91107    
PROX_SHOPPING_MALL   -206604.06   42840.60  -4.823 1.57e-06 ***
PROX_SUPERMARKET      -44991.80   77082.64  -0.584  0.55953    
PROX_BUS_STOP         683121.35  138353.28   4.938 8.85e-07 ***
NO_Of_UNITS             -231.18      89.03  -2.597  0.00951 ** 
FAMILY_FRIENDLY       140340.77   47020.55   2.985  0.00289 ** 
FREEHOLD              359913.01   49220.22   7.312 4.38e-13 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 755800 on 1417 degrees of freedom
Multiple R-squared:  0.6518,    Adjusted R-squared:  0.6474 
F-statistic: 147.4 on 18 and 1417 DF,  p-value: < 2.2e-16

5.4 Preparing Publication Quality Table : olsrr method

With reference to the report above, it is clear that not all the independent variables are statistically significant. We will revised the model by removing those variables which are not statistically significant.

Now, we are ready to calibrate the revised model by using the code chunk below.

condo.mlr1 <- lm(formula = SELLING_PRICE ~ AREA_SQM + AGE + 
                   PROX_CBD + PROX_CHILDCARE + PROX_ELDERLYCARE +
                   PROX_URA_GROWTH_AREA + PROX_MRT  + PROX_PARK + 
                   PROX_PRIMARY_SCH + PROX_SHOPPING_MALL    + PROX_BUS_STOP + 
                   NO_Of_UNITS + FAMILY_FRIENDLY + FREEHOLD,
                 data=condo_resale.sf) 
ols_regress(condo.mlr1)
                                Model Summary                                 
-----------------------------------------------------------------------------
R                            0.807       RMSE                     751998.679 
R-Squared                    0.651       MSE                571471422208.592 
Adj. R-Squared               0.647       Coef. Var                    43.168 
Pred R-Squared               0.638       AIC                       42966.758 
MAE                     414819.628       SBC                       43051.072 
-----------------------------------------------------------------------------
 RMSE: Root Mean Square Error 
 MSE: Mean Square Error 
 MAE: Mean Absolute Error 
 AIC: Akaike Information Criteria 
 SBC: Schwarz Bayesian Criteria 

                                     ANOVA                                       
--------------------------------------------------------------------------------
                    Sum of                                                      
                   Squares          DF         Mean Square       F         Sig. 
--------------------------------------------------------------------------------
Regression    1.512586e+15          14        1.080418e+14    189.059    0.0000 
Residual      8.120609e+14        1421    571471422208.592                      
Total         2.324647e+15        1435                                          
--------------------------------------------------------------------------------

                                               Parameter Estimates                                                
-----------------------------------------------------------------------------------------------------------------
               model           Beta    Std. Error    Std. Beta       t        Sig           lower          upper 
-----------------------------------------------------------------------------------------------------------------
         (Intercept)     527633.222    108183.223                   4.877    0.000     315417.244     739849.200 
            AREA_SQM      12777.523       367.479        0.584     34.771    0.000      12056.663      13498.382 
                 AGE     -24687.739      2754.845       -0.167     -8.962    0.000     -30091.739     -19283.740 
            PROX_CBD     -77131.323      5763.125       -0.263    -13.384    0.000     -88436.469     -65826.176 
      PROX_CHILDCARE    -318472.751    107959.512       -0.084     -2.950    0.003    -530249.889    -106695.613 
    PROX_ELDERLYCARE     185575.623     39901.864        0.090      4.651    0.000     107302.737     263848.510 
PROX_URA_GROWTH_AREA      39163.254     11754.829        0.060      3.332    0.001      16104.571      62221.936 
            PROX_MRT    -294745.107     56916.367       -0.112     -5.179    0.000    -406394.234    -183095.980 
           PROX_PARK     570504.807     65507.029        0.150      8.709    0.000     442003.938     699005.677 
    PROX_PRIMARY_SCH     159856.136     60234.599        0.062      2.654    0.008      41697.849     278014.424 
  PROX_SHOPPING_MALL    -220947.251     36561.832       -0.115     -6.043    0.000    -292668.213    -149226.288 
       PROX_BUS_STOP     682482.221    134513.243        0.134      5.074    0.000     418616.359     946348.082 
         NO_Of_UNITS       -245.480        87.947       -0.053     -2.791    0.005       -418.000        -72.961 
     FAMILY_FRIENDLY     146307.576     46893.021        0.057      3.120    0.002      54320.593     238294.560 
            FREEHOLD     350599.812     48506.485        0.136      7.228    0.000     255447.802     445751.821 
-----------------------------------------------------------------------------------------------------------------

5.5 Preparing Publication Quality Table : gtsummary method

The gtsummary package provides an elegant and flexible way to create publication-ready summary tables in R.

In the code chunk below, tbl_regression() is used to create a well formatted regression report.

tbl_regression(condo.mlr1, intercept = TRUE)
Characteristic Beta 95% CI1 p-value
(Intercept) 527,633 315,417, 739,849 <0.001
AREA_SQM 12,778 12,057, 13,498 <0.001
AGE -24,688 -30,092, -19,284 <0.001
PROX_CBD -77,131 -88,436, -65,826 <0.001
PROX_CHILDCARE -318,473 -530,250, -106,696 0.003
PROX_ELDERLYCARE 185,576 107,303, 263,849 <0.001
PROX_URA_GROWTH_AREA 39,163 16,105, 62,222 <0.001
PROX_MRT -294,745 -406,394, -183,096 <0.001
PROX_PARK 570,505 442,004, 699,006 <0.001
PROX_PRIMARY_SCH 159,856 41,698, 278,014 0.008
PROX_SHOPPING_MALL -220,947 -292,668, -149,226 <0.001
PROX_BUS_STOP 682,482 418,616, 946,348 <0.001
NO_Of_UNITS -245 -418, -73 0.005
FAMILY_FRIENDLY 146,308 54,321, 238,295 0.002
FREEHOLD 350,600 255,448, 445,752 <0.001
1 CI = Confidence Interval

With gtsummary package, model statistics can be included in the report by either appending them to the report table by using add_glance_table() or adding as a table source note by using add_glance_source_note() as shown in the code chunk below.

tbl_regression(condo.mlr1, 
               intercept = TRUE) %>% 
  add_glance_source_note(
    label = list(sigma ~ "\U03C3"),
    include = c(r.squared, adj.r.squared, 
                AIC, statistic,
                p.value, sigma))
Characteristic Beta 95% CI1 p-value
(Intercept) 527,633 315,417, 739,849 <0.001
AREA_SQM 12,778 12,057, 13,498 <0.001
AGE -24,688 -30,092, -19,284 <0.001
PROX_CBD -77,131 -88,436, -65,826 <0.001
PROX_CHILDCARE -318,473 -530,250, -106,696 0.003
PROX_ELDERLYCARE 185,576 107,303, 263,849 <0.001
PROX_URA_GROWTH_AREA 39,163 16,105, 62,222 <0.001
PROX_MRT -294,745 -406,394, -183,096 <0.001
PROX_PARK 570,505 442,004, 699,006 <0.001
PROX_PRIMARY_SCH 159,856 41,698, 278,014 0.008
PROX_SHOPPING_MALL -220,947 -292,668, -149,226 <0.001
PROX_BUS_STOP 682,482 418,616, 946,348 <0.001
NO_Of_UNITS -245 -418, -73 0.005
FAMILY_FRIENDLY 146,308 54,321, 238,295 0.002
FREEHOLD 350,600 255,448, 445,752 <0.001
R² = 0.651; Adjusted R² = 0.647; AIC = 42,967; Statistic = 189; p-value = <0.001; σ = 755,957
1 CI = Confidence Interval

5.5.1 Checking for multicollinearity

In this section, we would like to introduce you a fantastic R package specially programmed for performing OLS regression. It is called olsrr. It provides a collection of very useful methods for building better multiple linear regression models:

  • comprehensive regression output

  • residual diagnostics

  • measures of influence

  • heteroskedasticity tests

  • collinearity diagnostics

  • model fit assessment

  • variable contribution assessment

  • variable selection procedures

In the code chunk below, the ols_vif_tol() of olsrr package is used to test if there are sign of multicollinearity.

ols_vif_tol(condo.mlr1)
              Variables Tolerance      VIF
1              AREA_SQM 0.8728554 1.145665
2                   AGE 0.7071275 1.414172
3              PROX_CBD 0.6356147 1.573280
4        PROX_CHILDCARE 0.3066019 3.261559
5      PROX_ELDERLYCARE 0.6598479 1.515501
6  PROX_URA_GROWTH_AREA 0.7510311 1.331503
7              PROX_MRT 0.5236090 1.909822
8             PROX_PARK 0.8279261 1.207837
9      PROX_PRIMARY_SCH 0.4524628 2.210126
10   PROX_SHOPPING_MALL 0.6738795 1.483945
11        PROX_BUS_STOP 0.3514118 2.845664
12          NO_Of_UNITS 0.6901036 1.449058
13      FAMILY_FRIENDLY 0.7244157 1.380423
14             FREEHOLD 0.6931163 1.442759

Since the VIF of the independent variables are less than 10. We can safely conclude that there are no sign of multicollinearity among the independent variables.

5.5.2 Test for non-linearity

In multiple linear regression, it is important for us to test the assumption that linearity and additivity of the relationship between dependent and independent variables.

In the code chunk below, the ols_plot_resid_fit() of olsrr package is used to perform linearity assumption test.

ols_plot_resid_fit(condo.mlr1)

The figure above reveals that most of the data poitns are scattered around the 0 line, hence we can safely conclude that the relationships between the dependent variable and independent variables are linear.

5.5.3 Test for Normality Assumption

Lastly, the code chunk below uses ols_plot_resid_hist() of olsrr package to perform normality assumption test.

ols_plot_resid_hist(condo.mlr1)

The figure reveals that the residual of the multiple linear regression model (i.e. condo.mlr1) is resemble normal distribution.

If you prefer formal statistical test methods, the ols_test_normality() of olsrr package can be used as shown in the code chun below.

ols_test_normality(condo.mlr1)
Warning in ks.test.default(y, "pnorm", mean(y), sd(y)): ties should not be
present for the one-sample Kolmogorov-Smirnov test
-----------------------------------------------
       Test             Statistic       pvalue  
-----------------------------------------------
Shapiro-Wilk              0.6856         0.0000 
Kolmogorov-Smirnov        0.1366         0.0000 
Cramer-von Mises         121.0768        0.0000 
Anderson-Darling         67.9551         0.0000 
-----------------------------------------------

The summary table above reveals that the p-values of the four tests are way smaller than the alpha value of 0.05. Hence we will reject the null hypothesis and infer that there is statistical evidence that the residual are not normally distributed.

5.5.4 Testing for Spatial Autocorrelation

The hedonic model we try to build are using geographically referenced attributes, hence it is also important for us to visual the residual of the hedonic pricing model.

In order to perform spatial autocorrelation test, we need to convert condo_resale.sf from sf data frame into a SpatialPointsDataFrame.

First, we will export the residual of the hedonic pricing model and save it as a data frame.

mlr.output <- as.data.frame(condo.mlr1$residuals)

Next, we will join the newly created data frame with condo_resale.sf object.

condo_resale.res.sf <- cbind(condo_resale.sf, 
                        condo.mlr1$residuals) %>%
rename(`MLR_RES` = `condo.mlr1.residuals`)

Next, we will convert condo_resale.res.sf from simple feature object into a SpatialPointsDataFrame because spdep package can only process sp conformed spatial data objects.

The code chunk below will be used to perform the data conversion process.

condo_resale.sp <- as_Spatial(condo_resale.res.sf)
condo_resale.sp
class       : SpatialPointsDataFrame 
features    : 1436 
extent      : 14940.85, 43352.45, 24765.67, 48382.81  (xmin, xmax, ymin, ymax)
crs         : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs 
variables   : 23
names       : POSTCODE, SELLING_PRICE, AREA_SQM, AGE,    PROX_CBD, PROX_CHILDCARE, PROX_ELDERLYCARE, PROX_URA_GROWTH_AREA, PROX_HAWKER_MARKET, PROX_KINDERGARTEN,    PROX_MRT,   PROX_PARK, PROX_PRIMARY_SCH, PROX_TOP_PRIMARY_SCH, PROX_SHOPPING_MALL, ... 
min values  :    18965,        540000,       34,   0, 0.386916393,    0.004927023,      0.054508623,          0.214539508,        0.051817113,       0.004927023, 0.052779424, 0.029064164,      0.077106132,          0.077106132,                  0, ... 
max values  :   828833,       1.8e+07,      619,  37, 19.18042832,     3.46572633,      3.949157205,           9.15540001,        5.374348075,       2.229045366,  3.48037319,  2.16104919,      3.928989144,          6.748192062,        3.477433767, ... 

Next, we will use tmap package to display the distribution of the residuals on an interactive map.

The code churn below will turn on the interactive mode of tmap.

tmap_mode('view')
tmap mode set to interactive viewing
tm_shape(mpsz_svy21)+
  tmap_options(check.and.fix = TRUE) +
  tm_polygons(alpha = 0.4) +
tm_shape(condo_resale.res.sf) +  
  tm_dots(col = "MLR_RES",
          alpha = 0.6,
          style="quantile") +
  tm_view(set.zoom.limits = c(11,14))
Warning: The shape mpsz_svy21 is invalid (after reprojection). See
sf::st_is_valid
Variable(s) "MLR_RES" contains positive and negative values, so midpoint is set to 0. Set midpoint = NA to show the full spectrum of the color palette.
tmap_mode("plot")
tmap mode set to plotting

The figure above reveal that there is sign of spatial autocorrelation.

To prove that our observation is indeed true, the Moran’s I test will be performed

First, we will compute the distance-based weight matrix by using dnearneigh() function of spdep.

nb <- dnearneigh(coordinates(condo_resale.sp), 0, 1500, longlat = FALSE)
summary(nb)
Neighbour list object:
Number of regions: 1436 
Number of nonzero links: 66266 
Percentage nonzero weights: 3.213526 
Average number of links: 46.14624 
10 disjoint connected subgraphs
Link number distribution:

  1   3   5   7   9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24 
  3   3   9   4   3  15  10  19  17  45  19   5  14  29  19   6  35  45  18  47 
 25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44 
 16  43  22  26  21  11   9  23  22  13  16  25  21  37  16  18   8  21   4  12 
 45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64 
  8  36  18  14  14  43  11  12   8  13  12  13   4   5   6  12  11  20  29  33 
 65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84 
 15  20  10  14  15  15  11  16  12  10   8  19  12  14   9   8   4  13  11   6 
 85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 100 101 102 103 104 
  4   9   4   4   4   6   2  16   9   4   5   9   3   9   4   2   1   2   1   1 
105 106 107 108 109 110 112 116 125 
  1   5   9   2   1   3   1   1   1 
3 least connected regions:
193 194 277 with 1 link
1 most connected region:
285 with 125 links

Next, nb2listw() of spdep packge will be used to convert the output neighbours lists (i.e. nb) into a spatial weights.

nb_lw <- nb2listw(nb, style = 'W')
summary(nb_lw)
Characteristics of weights list object:
Neighbour list object:
Number of regions: 1436 
Number of nonzero links: 66266 
Percentage nonzero weights: 3.213526 
Average number of links: 46.14624 
10 disjoint connected subgraphs
Link number distribution:

  1   3   5   7   9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24 
  3   3   9   4   3  15  10  19  17  45  19   5  14  29  19   6  35  45  18  47 
 25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44 
 16  43  22  26  21  11   9  23  22  13  16  25  21  37  16  18   8  21   4  12 
 45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64 
  8  36  18  14  14  43  11  12   8  13  12  13   4   5   6  12  11  20  29  33 
 65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84 
 15  20  10  14  15  15  11  16  12  10   8  19  12  14   9   8   4  13  11   6 
 85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 100 101 102 103 104 
  4   9   4   4   4   6   2  16   9   4   5   9   3   9   4   2   1   2   1   1 
105 106 107 108 109 110 112 116 125 
  1   5   9   2   1   3   1   1   1 
3 least connected regions:
193 194 277 with 1 link
1 most connected region:
285 with 125 links

Weights style: W 
Weights constants summary:
     n      nn   S0       S1       S2
W 1436 2062096 1436 94.81916 5798.341

Next, lm.morantest() of spdep package will be used to perform Moran’s I test for residual spatial autocorrelation

lm.morantest(condo.mlr1, nb_lw)

    Global Moran I for regression residuals

data:  
model: lm(formula = SELLING_PRICE ~ AREA_SQM + AGE + PROX_CBD +
PROX_CHILDCARE + PROX_ELDERLYCARE + PROX_URA_GROWTH_AREA + PROX_MRT +
PROX_PARK + PROX_PRIMARY_SCH + PROX_SHOPPING_MALL + PROX_BUS_STOP +
NO_Of_UNITS + FAMILY_FRIENDLY + FREEHOLD, data = condo_resale.sf)
weights: nb_lw

Moran I statistic standard deviate = 24.366, p-value < 2.2e-16
alternative hypothesis: greater
sample estimates:
Observed Moran I      Expectation         Variance 
    1.438876e-01    -5.487594e-03     3.758259e-05 

The Global Moran’s I test for residual spatial autocorrelation shows that it’s p-value is less than 0.00000000000000022 which is less than the alpha value of 0.05. Hence, we will reject the null hypothesis that the residuals are randomly distributed.

Since the Observed Global Moran I = 0.1424418 which is greater than 0, we can infer than the residuals resemble cluster distribution..

6.0 Building Hedonic Pricing Models using GWmodel

6.1 Building Fixed Bandwidth GWR Model

6.2 Building Adaptive Bandwidth GWR Model

6.3 Visualising GWR Output

6.4 Converting SDF into sf data.frame

6.5 Visualising local R2

6.6 Visualising coefficient estimates